DebiChem Cheminformatics packages

The CDK is a library of Java classes used in computational and information chemistry and in bioinformatics. It includes renderers, file IO, SMILES generation/parsing, maximal common substructure algorithms, fingerprinting and much, much more.

OPSIN (Open Parser for Systematic IUPAC Nomenclature) converts IUPAC compound names to semantic chemical information and outputs a structure either as CML (Chemical Markup Language), SMILES, or InChI.

This package contains the Java library.

Open Babel is a chemical toolbox designed to speak the many languages of chemical data. It allows one to search, convert, analyze, or store data from molecular modeling, chemistry, solid-state materials, biochemistry, or related areas. Features include:

• Hydrogen addition and deletion
• Support for Molecular Mechanics
• Support for SMARTS molecular matching syntax
• Automatic feature perception (rings, bonds, hybridization, aromaticity)
• Flexible atom typer and perception of multiple bonds from atomic coordinates
• Gasteiger-Marsili partial charge calculation

File formats Open Babel supports include PDB, XYZ, CIF, CML, SMILES, MDL Molfile, ChemDraw, Gaussian, GAMESS, MOPAC and MPQC.

This package includes the following utilities:

• babel: Convert between various chemical file formats
• obenergy: Calculate the energy for a molecule
• obminimize: Optimize the geometry, minimize the energy for a molecule
• obgrep: Molecular search program using SMARTS pattern
• obgen: Generate 3D coordinates for a molecule
• obprop: Print standard molecular properties
• obfit: Superimpose two molecules based on a pattern
• obrotamer: Generate conformer/rotamer coordinates
• obconformer: Generate low-energy conformers
• obchiral: Print molecular chirality information
• obrotate: Rotate dihedral angle of molecules in batch mode
• obprobe: Create electrostatic probe grid

Chem-fingerprints is a set of formats and related tools for the storage, exchange, and search of cheminformatics fingerprint data sets.

It translates fingerprints from the OpenBabel and RDKIT and cheminformatics packages (as well as the proprietary OEChem package) into the binary FPS format.

Besides Python modules, it provides the following tools:

• sdf2fps - Extract fingerprint data from SD tags
• ob2fps - Use OpenBabel to generate fingerprints from structures
• rdkit2fps - Use RDKit to generate fingerprints from structures
• oe2fps - Use OEChem/OEGraphSim to generate fingerprints from structures
• simsearch - Do threshold or k-nearest neighbor Tanimoto similarity searches between two FPS files

Cinfoy provides a common Python interface to various cheminformatics toolkits. This makes it possible to use the complementary features of cheminformatics toolktis using a common interface. If functionality is provided by more than one toolkit, the Cinfony user can choose the implementation they prefer.

Cinfony supports the following toolkits:

• OpenBabel
• RDKit
• CDK
• Indigo

Cinfony also includes the Opsin module for translating IUPAC names to chemical data and the Webel web services module.

Fcms finds the maximum common substructure (MCS) of a group (or cluster) of chemical structures and report the result as a SMARTS string.

More specifically, the MCS found is a common edge subgraph, and not a common induced subgraph. Only connected MCSes are found.

Indigo is a C++ based organic chemistry and cheminformatics software environment. Features Include:

• Molecule and reaction rendering including SVG support
• Automatic layout for SMILES-represented molecules and reactions
• Canonical (isomeric) SMILES computation
• Exact matching, substructure matching, SMARTS matching
• Matching of tautomers and resonance structures
• Molecule fingerprinting, molecule similarity computation
• Fast enumeration of SSSR rings, subtrees, and edge sugraphs
• Molecular weight, molecular formula computation
• R-Group deconvolution and scaffold detection
• Computation of the exact maximum common substructure for an arbitrary amount of input structures
• Combinatorial chemistry
• Plugin support in the API

File formats Indigo support include MDL Mol, SDF, RDF, CML, SMILES and SMARTS.

This package contains the Python modules.

Open Babel is a chemical toolbox designed to speak the many languages of chemical data. It allows one to search, convert, analyze, or store data from molecular modeling, chemistry, solid-state materials, biochemistry, or related areas. Features include:

• Hydrogen addition and deletion
• Support for Molecular Mechanics
• Support for SMARTS molecular matching syntax
• Automatic feature perception (rings, bonds, hybridization, aromaticity)
• Flexible atom typer and perception of multiple bonds from atomic coordinates
• Gasteiger-Marsili partial charge calculation

File formats Open Babel supports include PDB, XYZ, CIF, CML, SMILES, MDL Molfile, ChemDraw, Gaussian, GAMESS, MOPAC and MPQC.

This package contains the Python binding.

RDKit is a Python/C++ based cheminformatics and machine-learning software environment. Features Include:

• Chemical reaction handling and transforms
• Substructure searching with SMARTS
• Canonical SMILES
• Molecule-molecule alignment
• Large number of molecular descriptors, including topological, compositional, EState, SlogP/SMR, VSA and Feature-map vectors
• Fragmentation using RECAP rules
• 2D coordinate generation and depiction, including constrained depiction
• 3D coordinate generation using geometry embedding
• UFF and MMFF94 forcefields
• Chirality support, including calculation of (R/S) stereochemistry codes
• 2D pharmacophore searching
• Fingerprinting, including Daylight-like, atom pairs, topological torsions, Morgan algorithm and MACCS keys
• Calculation of shape similarity
• Multi-molecule maximum common substructure
• Machine-learning via clustering and information theory algorithms
• Gasteiger-Marsili partial charge calculation

File formats RDKit supports include MDL Mol, PDB, SDF, TDT, SMILES and RDKit binary format.